1
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Fendt R, Ghallab A, Myllys M, Hofmann U, Hassan R, Hobloss Z, González D, Brackhagen L, Marchan R, Edlund K, Seddek AL, Abdelmageed N, Blank LM, Schlender JF, Holland CH, Hengstler JG, Kuepfer L. Increased sinusoidal export of drug glucuronides is a compensative mechanism in liver cirrhosis of mice. Front Pharmacol 2023; 14:1279357. [PMID: 38053838 PMCID: PMC10694292 DOI: 10.3389/fphar.2023.1279357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023] Open
Abstract
Rationale: Liver cirrhosis is known to affect drug pharmacokinetics, but the functional assessment of the underlying pathophysiological alterations in drug metabolism is difficult. Methods: Cirrhosis in mice was induced by repeated treatment with carbon tetrachloride for 12 months. A cocktail of six drugs was administered, and parent compounds as well as phase I and II metabolites were quantified in blood, bile, and urine in a time-dependent manner. Pharmacokinetics were modeled in relation to the altered expression of metabolizing enzymes. In discrepancy with computational predictions, a strong increase of glucuronides in blood was observed in cirrhotic mice compared to vehicle controls. Results: The deviation between experimental findings and computational simulations observed by analyzing different hypotheses could be explained by increased sinusoidal export and corresponded to increased expression of export carriers (Abcc3 and Abcc4). Formation of phase I metabolites and clearance of the parent compounds were surprisingly robust in cirrhosis, although the phase I enzymes critical for the metabolism of the administered drugs in healthy mice, Cyp1a2 and Cyp2c29, were downregulated in cirrhotic livers. RNA-sequencing revealed the upregulation of numerous other phase I metabolizing enzymes which may compensate for the lost CYP isoenzymes. Comparison of genome-wide data of cirrhotic mouse and human liver tissue revealed similar features of expression changes, including increased sinusoidal export and reduced uptake carriers. Conclusion: Liver cirrhosis leads to increased blood concentrations of glucuronides because of increased export from hepatocytes into the sinusoidal blood. Although individual metabolic pathways are massively altered in cirrhosis, the overall clearance of the parent compounds was relatively robust due to compensatory mechanisms.
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Affiliation(s)
- Rebekka Fendt
- Institute for Systems Medicine with Focus on Organ Interaction, University Hospital RWTH Aachen, Aachen, Germany
| | - Ahmed Ghallab
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Maiju Myllys
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and University of Tübingen, Stuttgart, Germany
| | - Reham Hassan
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Zaynab Hobloss
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Daniela González
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Lisa Brackhagen
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Rosemarie Marchan
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Abdel-Latif Seddek
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Noha Abdelmageed
- Department of Pharmacology, Faculty of Veterinary Medicine, Sohag University, Sohag, Egypt
| | - Lars M. Blank
- Institute of Applied Microbiology—iAMB, Aachen Biology and Biotechnology—ABBt, RWTH Aachen University, Aachen, Germany
| | - Jan-Frederik Schlender
- Pharmacometrics, Research and Development, Pharmaceuticals, Bayer AG, Leverkusen, Germany
| | - Christian H. Holland
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, Dortmund, Germany
| | - Lars Kuepfer
- Institute for Systems Medicine with Focus on Organ Interaction, University Hospital RWTH Aachen, Aachen, Germany
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2
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Hammad S, Ogris C, Othman A, Erdoesi P, Schmidt-Heck W, Biermayer I, Helm B, Gao Y, Piorońska W, Holland CH, D'Alessandro LA, de la Torre C, Sticht C, Al Aoua S, Theis FJ, Bantel H, Ebert MP, Klingmüller U, Hengstler JG, Dooley S, Mueller NS. Tolerance of repeated toxic injuries of murine livers is associated with steatosis and inflammation. Cell Death Dis 2023; 14:414. [PMID: 37438332 DOI: 10.1038/s41419-023-05855-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 04/13/2023] [Accepted: 05/05/2023] [Indexed: 07/14/2023]
Abstract
The human liver has a remarkable capacity to regenerate and thus compensate over decades for fibrosis caused by toxic chemicals, drugs, alcohol, or malnutrition. To date, no protective mechanisms have been identified that help the liver tolerate these repeated injuries. In this study, we revealed dysregulation of lipid metabolism and mild inflammation as protective mechanisms by studying longitudinal multi-omic measurements of liver fibrosis induced by repeated CCl4 injections in mice (n = 45). Based on comprehensive proteomics, transcriptomics, blood- and tissue-level profiling, we uncovered three phases of early disease development-initiation, progression, and tolerance. Using novel multi-omic network analysis, we identified multi-level mechanisms that are significantly dysregulated in the injury-tolerant response. Public data analysis shows that these profiles are altered in human liver diseases, including fibrosis and early cirrhosis stages. Our findings mark the beginning of the tolerance phase as the critical switching point in liver response to repetitive toxic doses. After fostering extracellular matrix accumulation as an acute response, we observe a deposition of tiny lipid droplets in hepatocytes only in the Tolerant phase. Our comprehensive study shows that lipid metabolism and mild inflammation may serve as biomarkers and are putative functional requirements to resist further disease progression.
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Affiliation(s)
- Seddik Hammad
- Molecular Hepatology Section, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Department of Forensic Medicine and Veterinary Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt.
| | - Christoph Ogris
- Institute of Computational Biology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Amnah Othman
- Department of Toxicology, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Dortmund, Germany
| | - Pia Erdoesi
- Molecular Hepatology Section, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Wolfgang Schmidt-Heck
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany
| | - Ina Biermayer
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Barbara Helm
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Yan Gao
- Molecular Hepatology Section, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Weronika Piorońska
- Molecular Hepatology Section, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Christian H Holland
- Department of Toxicology, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Dortmund, Germany
| | - Lorenza A D'Alessandro
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Carolina de la Torre
- Core Facility Next Generation Sequencing, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carsten Sticht
- Core Facility Next Generation Sequencing, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Sherin Al Aoua
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Strasse 1, Hannover, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Heike Bantel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Strasse 1, Hannover, Germany
| | - Matthias P Ebert
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Clinical Cooperation Unit Healthy Metabolism, Center of Preventive Medicine and Digital Health, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), INF 280, Heidelberg, Germany
| | - Jan G Hengstler
- Department of Toxicology, Leibniz Research Centre for Working Environment and Human Factors (IfADo), Dortmund, Germany
| | - Steven Dooley
- Molecular Hepatology Section, Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nikola S Mueller
- Institute of Computational Biology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
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3
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Schneider KM, Mohs A, Gui W, Galvez EJC, Candels LS, Hoenicke L, Muthukumarasamy U, Holland CH, Elfers C, Kilic K, Schneider CV, Schierwagen R, Strnad P, Wirtz TH, Marschall HU, Latz E, Lelouvier B, Saez-Rodriguez J, de Vos W, Strowig T, Trebicka J, Trautwein C. Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment. Nat Commun 2022; 13:3964. [PMID: 35803930 PMCID: PMC9270328 DOI: 10.1038/s41467-022-31312-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/13/2022] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide, and therapeutic options for advanced HCC are limited. Here, we observe that intestinal dysbiosis affects antitumor immune surveillance and drives liver disease progression towards cancer. Dysbiotic microbiota, as seen in Nlrp6−/− mice, induces a Toll-like receptor 4 dependent expansion of hepatic monocytic myeloid-derived suppressor cells (mMDSC) and suppression of T-cell abundance. This phenotype is transmissible via fecal microbiota transfer and reversible upon antibiotic treatment, pointing to the high plasticity of the tumor microenvironment. While loss of Akkermansia muciniphila correlates with mMDSC abundance, its reintroduction restores intestinal barrier function and strongly reduces liver inflammation and fibrosis. Cirrhosis patients display increased bacterial abundance in hepatic tissue, which induces pronounced transcriptional changes, including activation of fibro-inflammatory pathways as well as circuits mediating cancer immunosuppression. This study demonstrates that gut microbiota closely shapes the hepatic inflammatory microenvironment opening approaches for cancer prevention and therapy. Steatohepatitis is a chronic hepatic inflammation associated with increased risk of hepatocellular carcinoma progression. Here the authors show that intestinal dysbiosis in mice lacking the inflammasome sensor molecule NLRP6 aggravates steatohepatitis and accelerates liver cancer progression, a process that can be delayed by antibiotic treatment.
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Affiliation(s)
- Kai Markus Schneider
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Antje Mohs
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Wenfang Gui
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Eric J C Galvez
- Helmholtz Centre for Infection Research, Braunschweig, Germany and Hannover Medical School, Hannover, Germany
| | | | - Lisa Hoenicke
- Helmholtz Centre for Infection Research, Braunschweig, Germany and Hannover Medical School, Hannover, Germany
| | - Uthayakumar Muthukumarasamy
- Helmholtz Centre for Infection Research, Braunschweig, Germany and Hannover Medical School, Hannover, Germany
| | - Christian H Holland
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany.,Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany
| | - Carsten Elfers
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Konrad Kilic
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Carolin Victoria Schneider
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany.,The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Robert Schierwagen
- European Foundation for the Study of Chronic Liver Failure (EF-CLIF), 08021, Barcelona, Spain.,Translational Hepatology, Department of Internal Medicine I, Goethe University Frankfurt, 60323, Frankfurt, Germany
| | - Pavel Strnad
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Theresa H Wirtz
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Hanns-Ulrich Marschall
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Eicke Latz
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127, Bonn, Germany.,Department of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.,German Center for Neurodegenerative Diseases, 53127, Bonn, Germany
| | | | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany.,Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany
| | - Willem de Vos
- Laboratory of Microbiology, Wageningen University, 6708 WE, Wageningen, The Netherlands.,Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, P.O. Box 63, 00014, Helsinki, Finland
| | - Till Strowig
- Helmholtz Centre for Infection Research, Braunschweig, Germany and Hannover Medical School, Hannover, Germany
| | - Jonel Trebicka
- European Foundation for the Study of Chronic Liver Failure (EF-CLIF), 08021, Barcelona, Spain.,Translational Hepatology, Department of Internal Medicine I, Goethe University Frankfurt, 60323, Frankfurt, Germany
| | - Christian Trautwein
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany.
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4
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Badia-i-Mompel P, Vélez Santiago J, Braunger J, Geiss C, Dimitrov D, Müller-Dott S, Taus P, Dugourd A, Holland CH, Ramirez Flores RO, Saez-Rodriguez J. decoupleR: ensemble of computational methods to infer biological activities from omics data. Bioinform Adv 2022; 2:vbac016. [PMID: 36699385 PMCID: PMC9710656 DOI: 10.1093/bioadv/vbac016] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 02/01/2023]
Abstract
Summary Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present decoupleR, a Bioconductor and Python package containing computational methods to extract these activities within a unified framework. decoupleR allows us to flexibly run any method with a given resource, including methods that leverage mode of regulation and weights of interactions, which are not present in other frameworks. Moreover, it leverages OmniPath, a meta-resource comprising over 100 databases of prior knowledge. Using decoupleR, we evaluated the performance of methods on transcriptomic and phospho-proteomic perturbation experiments. Our findings suggest that simple linear models and the consensus score across top methods perform better than other methods at predicting perturbed regulators. Availability and implementation decoupleR's open-source code is available in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/decoupleR.html) for R and in GitHub (https://github.com/saezlab/decoupler-py) for Python. The code to reproduce the results is in GitHub (https://github.com/saezlab/decoupleR_manuscript) and the data in Zenodo (https://zenodo.org/record/5645208). Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Pau Badia-i-Mompel
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg 69120, Germany,Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg 69120, Germany
| | - Jesús Vélez Santiago
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg 69120, Germany,Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg 69120, Germany
| | - Jana Braunger
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg 69120, Germany,Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg 69120, Germany
| | - Celina Geiss
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg 69120, Germany,Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg 69120, Germany
| | - Daniel Dimitrov
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg 69120, Germany,Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg 69120, Germany
| | - Sophia Müller-Dott
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg 69120, Germany,Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg 69120, Germany
| | - Petr Taus
- Central European Institute of Technology, Masaryk University, Brno 601, Czechia
| | - Aurelien Dugourd
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg 69120, Germany,Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg 69120, Germany
| | - Christian H Holland
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg 69120, Germany,Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg 69120, Germany
| | - Ricardo O Ramirez Flores
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg 69120, Germany,Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg 69120, Germany
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant, Heidelberg 69120, Germany,Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg 69120, Germany,To whom correspondence should be addressed.
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5
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Abstract
Motivation Omics data are broadly used to get a snapshot of the molecular status of cells. In particular, changes in omics can be used to estimate the activity of pathways, transcription factors and kinases based on known regulated targets, that we call footprints. Then the molecular paths driving these activities can be estimated using causal reasoning on large signalling networks. Results We have developed FUNKI, a FUNctional toolKIt for footprint analysis. It provides a user-friendly interface for an easy and fast analysis of transcriptomics, phosphoproteomics and metabolomics data, either from bulk or single-cell experiments. FUNKI also features different options to visualize the results and run post-analyses, and is mirrored as a scripted version in R. Availability and implementation FUNKI is a free and open-source application built on R and Shiny, available at https://github.com/saezlab/ShinyFUNKI and https://saezlab.shinyapps.io/funki/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rosa Hernansaiz-Ballesteros
- Institute for Computational Biomedicine, Heidelberg University, Heidelberg University Hospital, Faculty of Medicine, Bioquant, Heidelberg 69120, Germany
| | - Christian H Holland
- Institute for Computational Biomedicine, Heidelberg University, Heidelberg University Hospital, Faculty of Medicine, Bioquant, Heidelberg 69120, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg 69120, Germany
| | - Aurelien Dugourd
- Institute for Computational Biomedicine, Heidelberg University, Heidelberg University Hospital, Faculty of Medicine, Bioquant, Heidelberg 69120, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg 69120, Germany
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6
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Ghallab A, Myllys M, Friebel A, Duda J, Edlund K, Halilbasic E, Vucur M, Hobloss Z, Brackhagen L, Begher-Tibbe B, Hassan R, Burke M, Genc E, Frohwein LJ, Hofmann U, Holland CH, González D, Keller M, Seddek AL, Abbas T, Mohammed ESI, Teufel A, Itzel T, Metzler S, Marchan R, Cadenas C, Watzl C, Nitsche MA, Kappenberg F, Luedde T, Longerich T, Rahnenführer J, Hoehme S, Trauner M, Hengstler JG. Spatio-Temporal Multiscale Analysis of Western Diet-Fed Mice Reveals a Translationally Relevant Sequence of Events during NAFLD Progression. Cells 2021; 10:cells10102516. [PMID: 34685496 PMCID: PMC8533774 DOI: 10.3390/cells10102516] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 12/12/2022] Open
Abstract
Mouse models of non-alcoholic fatty liver disease (NAFLD) are required to define therapeutic targets, but detailed time-resolved studies to establish a sequence of events are lacking. Here, we fed male C57Bl/6N mice a Western or standard diet over 48 weeks. Multiscale time-resolved characterization was performed using RNA-seq, histopathology, immunohistochemistry, intravital imaging, and blood chemistry; the results were compared to human disease. Acetaminophen toxicity and ammonia metabolism were additionally analyzed as functional readouts. We identified a sequence of eight key events: formation of lipid droplets; inflammatory foci; lipogranulomas; zonal reorganization; cell death and replacement proliferation; ductular reaction; fibrogenesis; and hepatocellular cancer. Functional changes included resistance to acetaminophen and altered nitrogen metabolism. The transcriptomic landscape was characterized by two large clusters of monotonously increasing or decreasing genes, and a smaller number of 'rest-and-jump genes' that initially remained unaltered but became differentially expressed only at week 12 or later. Approximately 30% of the genes altered in human NAFLD are also altered in the present mouse model and an increasing overlap with genes altered in human HCC occurred at weeks 30-48. In conclusion, the observed sequence of events recapitulates many features of human disease and offers a basis for the identification of therapeutic targets.
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Affiliation(s)
- Ahmed Ghallab
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt;
- Correspondence: (A.G.); (J.G.H.); Tel.: +49-0231-1084-356 (A.G.); +49-0231-1084-348 (J.G.H.)
| | - Maiju Myllys
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Adrian Friebel
- Institute of Computer Science & Saxonian Incubator for Clinical Research (SIKT), University of Leipzig, Haertelstr. 16-18, 04107 Leipzig, Germany; (A.F.); (S.H.)
| | - Julia Duda
- Department of Statistics, TU Dortmund University, 44227 Dortmund, Germany; (J.D.); (F.K.); (J.R.)
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Emina Halilbasic
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (E.H.); (M.T.)
| | - Mihael Vucur
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty at Heinrich-Heine-University, University Hospital Duesseldorf, 40225 Dusseldorf, Germany; (M.V.); (T.L.)
| | - Zaynab Hobloss
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Lisa Brackhagen
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Brigitte Begher-Tibbe
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Reham Hassan
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt;
| | - Michael Burke
- MRI Unit, Leibniz Research Centre for Working Environment and Human Factors, Department of Psychology and Neurosciences, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.B.); (E.G.)
| | - Erhan Genc
- MRI Unit, Leibniz Research Centre for Working Environment and Human Factors, Department of Psychology and Neurosciences, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.B.); (E.G.)
| | | | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, University of Tübingen, Auerbachstr. 112, 70376 Stuttgart, Germany;
| | - Christian H. Holland
- Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine, Bioquant—Im Neuenheimer Feld 267, 69120 Heidelberg, Germany;
| | - Daniela González
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Magdalena Keller
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Abdel-latif Seddek
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt;
| | - Tahany Abbas
- Histology Department, Faculty of Medicine, South Valley University, Qena 83523, Egypt;
| | - Elsayed S. I. Mohammed
- Department of Histology and Cytology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt;
| | - Andreas Teufel
- Department of Medicine I, University Hospital, 93053 Regensburg, Germany; (A.T.); (T.I.)
| | - Timo Itzel
- Department of Medicine I, University Hospital, 93053 Regensburg, Germany; (A.T.); (T.I.)
| | - Sarah Metzler
- Leibniz Research Centre for Working Environment and Human Factors, Department of Immunology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (S.M.); (C.W.)
| | - Rosemarie Marchan
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Cristina Cadenas
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
| | - Carsten Watzl
- Leibniz Research Centre for Working Environment and Human Factors, Department of Immunology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (S.M.); (C.W.)
| | - Michael A. Nitsche
- Leibniz Research Centre for Working Environment and Human Factors, Department of Psychology and Neurosciences, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany;
| | - Franziska Kappenberg
- Department of Statistics, TU Dortmund University, 44227 Dortmund, Germany; (J.D.); (F.K.); (J.R.)
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty at Heinrich-Heine-University, University Hospital Duesseldorf, 40225 Dusseldorf, Germany; (M.V.); (T.L.)
| | - Thomas Longerich
- Translational Gastrointestinal Pathology, Institute of Pathology, University Hospital Heidelberg, D-69120 Heidelberg, Germany;
| | - Jörg Rahnenführer
- Department of Statistics, TU Dortmund University, 44227 Dortmund, Germany; (J.D.); (F.K.); (J.R.)
| | - Stefan Hoehme
- Institute of Computer Science & Saxonian Incubator for Clinical Research (SIKT), University of Leipzig, Haertelstr. 16-18, 04107 Leipzig, Germany; (A.F.); (S.H.)
| | - Michael Trauner
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria; (E.H.); (M.T.)
| | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Department of Toxicology, Technical University Dortmund, Ardeystr. 67, 44139 Dortmund, Germany; (M.M.); (K.E.); (Z.H.); (L.B.); (B.B.-T.); (R.H.); (D.G.); (M.K.); (R.M.); (C.C.)
- Correspondence: (A.G.); (J.G.H.); Tel.: +49-0231-1084-356 (A.G.); +49-0231-1084-348 (J.G.H.)
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Holland CH, Ramirez Flores RO, Myllys M, Hassan R, Edlund K, Hofmann U, Marchan R, Cadenas C, Reinders J, Hoehme S, Seddek AL, Dooley S, Keitel V, Godoy P, Begher-Tibbe B, Trautwein C, Rupp C, Mueller S, Longerich T, Hengstler JG, Saez-Rodriguez J, Ghallab A. Transcriptomic Cross-Species Analysis of Chronic Liver Disease Reveals Consistent Regulation Between Humans and Mice. Hepatol Commun 2021; 6:161-177. [PMID: 34558834 PMCID: PMC8710791 DOI: 10.1002/hep4.1797] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022] Open
Abstract
Mouse models are frequently used to study chronic liver diseases (CLDs). To assess their translational relevance, we quantified the similarity of commonly used mouse models to human CLDs based on transcriptome data. Gene‐expression data from 372 patients were compared with data from acute and chronic mouse models consisting of 227 mice, and additionally to nine published gene sets of chronic mouse models. Genes consistently altered in humans and mice were mapped to liver cell types based on single‐cell RNA‐sequencing data and validated by immunostaining. Considering the top differentially expressed genes, the similarity between humans and mice varied among the mouse models and depended on the period of damage induction. The highest recall (0.4) and precision (0.33) were observed for the model with 12‐months damage induction by CCl4 and by a Western diet, respectively. Genes consistently up‐regulated between the chronic CCl4 model and human CLDs were enriched in inflammatory and developmental processes, and mostly mapped to cholangiocytes, macrophages, and endothelial and mesenchymal cells. Down‐regulated genes were enriched in metabolic processes and mapped to hepatocytes. Immunostaining confirmed the regulation of selected genes and their cell type specificity. Genes that were up‐regulated in both acute and chronic models showed higher recall and precision with respect to human CLDs than exclusively acute or chronic genes. Conclusion: Similarly regulated genes in human and mouse CLDs were identified. Despite major interspecies differences, mouse models detected 40% of the genes significantly altered in human CLD. The translational relevance of individual genes can be assessed at https://saezlab.shinyapps.io/liverdiseaseatlas/.
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Affiliation(s)
- Christian H Holland
- Institute of Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Joint Research Centre for Computational Biomedicine, Faculty of Medicine, RWTH Aachen University, Aachen, Germany.,Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Ricardo O Ramirez Flores
- Institute of Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Maiju Myllys
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Reham Hassan
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany.,Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Karolina Edlund
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Rosemarie Marchan
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Cristina Cadenas
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Jörg Reinders
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Stefan Hoehme
- Institute for Computer Science & Saxonian Incubator for Clinical Research, University of Leipzig, Leipzig, Germany
| | - Abdel-Latif Seddek
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Steven Dooley
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Verena Keitel
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty at Heinrich-Heine-University, Düsseldorf, Germany
| | - Patricio Godoy
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Brigitte Begher-Tibbe
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Christian Trautwein
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Christian Rupp
- Internal Medicine IV, University Hospital Heidelberg, Heidelberg, Germany
| | - Sebastian Mueller
- Salem Medical Center and Center for Alcohol Research, University of Heidelberg, Heidelberg, Germany
| | - Thomas Longerich
- Translational Gastrointestinal Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Jan G Hengstler
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Julio Saez-Rodriguez
- Institute of Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany.,Joint Research Centre for Computational Biomedicine, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Ahmed Ghallab
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany.,Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
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8
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Ramirez Flores RO, Lanzer JD, Holland CH, Leuschner F, Most P, Schultz J, Levinson RT, Saez‐Rodriguez J. Consensus Transcriptional Landscape of Human End-Stage Heart Failure. J Am Heart Assoc 2021; 10:e019667. [PMID: 33787284 PMCID: PMC8174362 DOI: 10.1161/jaha.120.019667] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Background Transcriptomic studies have contributed to fundamental knowledge of myocardial remodeling in human heart failure (HF). However, the key HF genes reported are often inconsistent between studies, and systematic efforts to integrate evidence from multiple patient cohorts are lacking. Here, we aimed to provide a framework for comprehensive comparison and analysis of publicly available data sets resulting in an unbiased consensus transcriptional signature of human end-stage HF. Methods and Results We curated and uniformly processed 16 public transcriptomic studies of left ventricular samples from 263 healthy and 653 failing human hearts. First, we evaluated the degree of consistency between studies by using linear classifiers and overrepresentation analysis. Then, we meta-analyzed the deregulation of 14 041 genes to extract a consensus signature of HF. Finally, to functionally characterize this signature, we estimated the activities of 343 transcription factors, 14 signaling pathways, and 182 micro RNAs, as well as the enrichment of 5998 biological processes. Machine learning approaches revealed conserved disease patterns across all studies independent of technical differences. These consistent molecular changes were prioritized with a meta-analysis, functionally characterized and validated on external data. We provide all results in a free public resource (https://saezlab.shinyapps.io/reheat/) and exemplified usage by deciphering fetal gene reprogramming and tracing the potential myocardial origin of the plasma proteome markers in patients with HF. Conclusions Even though technical and sampling variability confound the identification of differentially expressed genes in individual studies, we demonstrated that coordinated molecular responses during end-stage HF are conserved. The presented resource is crucial to complement findings in independent studies and decipher fundamental changes in failing myocardium.
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Affiliation(s)
- Ricardo O. Ramirez Flores
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
| | - Jan D. Lanzer
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Christian H. Holland
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Florian Leuschner
- Department of CardiologyMedical University HospitalHeidelbergGermany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/MannheimHeidelbergGermany
| | - Patrick Most
- Department of CardiologyMedical University HospitalHeidelbergGermany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/MannheimHeidelbergGermany
- Center for Translational MedicineJefferson UniversityPhiladelphiaPA
| | - Jobst‐Hendrik Schultz
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Rebecca T. Levinson
- Informatics for LifeHeidelbergGermany
- Department of General Internal Medicine and PsychosomaticsHeidelberg University HospitalHeidelbergGermany
| | - Julio Saez‐Rodriguez
- Faculty of Medicine, and Heidelberg University HospitalInstitute for Computational BiomedicineBioquantHeidelberg UniversityHeidelbergGermany
- Informatics for LifeHeidelbergGermany
- Faculty of MedicineJoint Research Centre for Computational Biomedicine (JRC‐COMBINE)RWTH Aachen UniversityAachenGermany
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Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J. Corrigendum: Benchmark and integration of resources for the estimation of human transcription factor activities. Genome Res 2021; 31:745. [PMID: 33795376 DOI: 10.1101/gr.275408.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Mohs A, Otto T, Schneider KM, Peltzer M, Boekschoten M, Holland CH, Hudert CA, Kalveram L, Wiegand S, Saez-Rodriguez J, Longerich T, Hengstler JG, Trautwein C. Hepatocyte-specific NRF2 activation controls fibrogenesis and carcinogenesis in steatohepatitis. J Hepatol 2021; 74:638-648. [PMID: 33342543 DOI: 10.1016/j.jhep.2020.09.037] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS In chronic liver diseases, inflammation induces oxidative stress and thus may contribute to the progression of liver injury, fibrosis, and carcinogenesis. The KEAP1/NRF2 axis is a major regulator of cellular redox balance. In the present study, we investigated whether the KEAP1/NRF2 system is involved in liver disease progression in humans and mice. METHODS The clinical relevance of oxidative stress was investigated by liver RNA sequencing in a well-characterized cohort of patients with non-alcoholic fatty liver disease (n = 63) and correlated with histological and clinical parameters. For functional analysis, hepatocyte-specific Nemo knockout (NEMOΔhepa) mice were crossed with hepatocyte-specific Keap1 knockout (KEAP1Δhepa) mice. RESULTS Immunohistochemical analysis of human liver sections showed increased oxidative stress and high NRF2 expression in patients with chronic liver disease. RNA sequencing of liver samples in a human pediatric NAFLD cohort revealed a significant increase of NRF2 activation correlating with the grade of inflammation, but not with the grade of steatosis, which could be confirmed in a second adult NASH cohort. In mice, microarray analysis revealed that Keap1 deletion induces NRF2 target genes involved in glutathione metabolism and xenobiotic stress (e.g., Nqo1). Furthermore, deficiency of one of the most important antioxidants, glutathione (GSH), in NEMOΔhepa livers was rescued after deleting Keap1. As a consequence, NEMOΔhepa/KEAP1Δhepa livers showed reduced apoptosis compared to NEMOΔhepa livers as well as a dramatic downregulation of genes involved in cell cycle regulation and DNA replication. Consequently, NEMOΔhepa/KEAP1Δhepa compared to NEMOΔhepa livers displayed decreased fibrogenesis, lower tumor incidence, reduced tumor number, and decreased tumor size. CONCLUSIONS NRF2 activation in patients with non-alcoholic steatohepatitis correlates with the grade of inflammation, but not steatosis. Functional analysis in mice demonstrated that NRF2 activation in chronic liver disease is protective by ameliorating fibrogenesis, initiation and progression of hepatocellular carcinogenesis. LAY SUMMARY The KEAP1 (Kelch-like ECH-associated protein-1)/NRF2 (erythroid 2-related factor 2) axis has a major role in regulating cellular redox balance. Herein, we show that NRF2 activity correlates with the grade of inflammation in patients with non-alcoholic steatohepatitis. Functional studies in mice actually show that NRF2 activation, resulting from KEAP1 deletion, protects against fibrosis and cancer.
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Affiliation(s)
- Antje Mohs
- Department of Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Tobias Otto
- Department of Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Kai Markus Schneider
- Department of Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Mona Peltzer
- Department of Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Mark Boekschoten
- Department of Agrotechnology and Food Sciences, University Wageningen, Wageningen, the Netherlands
| | - Christian H Holland
- Faculty of Medicine, Institute of Computational Biomedicine, Heidelberg University, Bioquant, Heidelberg, Germany; Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany; Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund (IfADo), Dortmund, Germany
| | - Christian A Hudert
- Department of Pediatric Gastroenterology, Charité - Universitätsmedizin Berlin, Germany
| | - Laura Kalveram
- Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Susanna Wiegand
- Center for Chronically Sick Children, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Institute of Computational Biomedicine, Heidelberg University, Bioquant, Heidelberg, Germany; Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
| | - Thomas Longerich
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Jan G Hengstler
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund (IfADo), Dortmund, Germany
| | - Christian Trautwein
- Department of Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany.
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Holland CH, Szalai B, Saez-Rodriguez J. Transfer of regulatory knowledge from human to mouse for functional genomics analysis. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2020; 1863:194431. [DOI: 10.1016/j.bbagrm.2019.194431] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/31/2019] [Accepted: 09/01/2019] [Indexed: 12/24/2022]
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Holland CH, Tanevski J, Perales-Patón J, Gleixner J, Kumar MP, Mereu E, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez J. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. Genome Biol 2020; 21:36. [PMID: 32051003 PMCID: PMC7017576 DOI: 10.1186/s13059-020-1949-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way. RESULTS To address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. We also provide the benchmark data for further use by the community. CONCLUSIONS Our analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used.
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Affiliation(s)
- Christian H Holland
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany
| | - Jovan Tanevski
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
- Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Javier Perales-Patón
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
| | - Jan Gleixner
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Manu P Kumar
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Elisabetta Mereu
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Brian A Joughin
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Biology, MIT, Cambridge, MA, USA
| | - Oliver Stegle
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bence Szalai
- Faculty of Medicine, Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany.
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany.
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13
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Szalai B, Subramanian V, Holland CH, Alföldi R, Puskás LG, Saez-Rodriguez J. Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction. Nucleic Acids Res 2019; 47:10010-10026. [PMID: 31552418 PMCID: PMC6821211 DOI: 10.1093/nar/gkz805] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 01/27/2023] Open
Abstract
Transcriptional perturbation signatures are valuable data sources for functional genomics. Linking perturbation signatures to screenings opens the possibility to model cellular phenotypes from expression data and to identify efficacious drugs. We linked perturbation transcriptomics data from the LINCS-L1000 project with cell viability information upon genetic (Achilles project) and chemical (CTRP screen) perturbations yielding more than 90 000 signature–viability pairs. An integrated analysis showed that the cell viability signature is a major factor underlying perturbation signatures. The signature is linked to transcription factors regulating cell death, proliferation and division time. We used the cell viability–signature relationship to predict viability from transcriptomics signatures, and identified and validated compounds that induce cell death in tumor cell lines. We showed that cellular toxicity can lead to unexpected similarity of signatures, confounding mechanism of action discovery. Consensus compound signatures predicted cell-specific drug sensitivity, even if the signature is not measured in the same cell line, and outperformed conventional drug-specific features. Our results can help in understanding mechanisms behind cell death and removing confounding factors of transcriptomic perturbation screens. To interactively browse our results and predict cell viability in new gene expression samples, we developed CEVIChE (CEll VIability Calculator from gene Expression; https://saezlab.shinyapps.io/ceviche/).
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Affiliation(s)
- Bence Szalai
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany.,Semmelweis University, Faculty of Medicine, Department of Physiology, H-1094 Budapest, Hungary
| | - Vigneshwari Subramanian
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany
| | - Christian H Holland
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany.,Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
| | | | | | - Julio Saez-Rodriguez
- RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany.,Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany
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Ghallab A, Myllys M, H. Holland C, Zaza A, Murad W, Hassan R, A. Ahmed Y, Abbas T, A. Abdelrahim E, Schneider KM, Matz-Soja M, Reinders J, Gebhardt R, Berres ML, Hatting M, Drasdo D, Saez-Rodriguez J, Trautwein C, G. Hengstler J. Influence of Liver Fibrosis on Lobular Zonation. Cells 2019; 8:E1556. [PMID: 31810365 PMCID: PMC6953125 DOI: 10.3390/cells8121556] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/18/2022] Open
Abstract
Little is known about how liver fibrosis influences lobular zonation. To address this question, we used three mouse models of liver fibrosis, repeated CCl4 administration for 2, 6 and 12 months to induce pericentral damage, as well as bile duct ligation (21 days) and mdr2-/- mice to study periportal fibrosis. Analyses were performed by RNA-sequencing, immunostaining of zonated proteins and image analysis. RNA-sequencing demonstrated a significant enrichment of pericentral genes among genes downregulated by CCl4; vice versa, periportal genes were enriched among the upregulated genes. Immunostaining showed an almost complete loss of pericentral proteins, such as cytochrome P450 enzymes and glutamine synthetase, while periportal proteins, such as arginase 1 and CPS1 became expressed also in pericentral hepatocytes. This pattern of fibrosis-associated 'periportalization' was consistently observed in all three mouse models and led to complete resistance to hepatotoxic doses of acetaminophen (200 mg/kg). Characterization of the expression response identified the inflammatory pathways TGFβ, NFκB, TNFα, and transcription factors NFKb1, Stat1, Hif1a, Trp53, and Atf1 among those activated, while estrogen-associated pathways, Hnf4a and Hnf1a, were decreased. In conclusion, liver fibrosis leads to strong alterations of lobular zonation, where the pericentral region adopts periportal features. Beside adverse consequences, periportalization supports adaptation to repeated doses of hepatotoxic compounds.
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Affiliation(s)
- Ahmed Ghallab
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, 44139 Dortmund, Germany, (A.Z.); , (J.R.); (D.D.)
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Maiju Myllys
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, 44139 Dortmund, Germany, (A.Z.); , (J.R.); (D.D.)
| | - Christian H. Holland
- Faculty of Medicine, Institute of Computational Biomedicine, Heidelberg University, Bioquant—Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; (C.H.H.); (J.S.-R.)
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Pauwelsstrasse 19, 52074 Aachen, Germany
| | - Ayham Zaza
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, 44139 Dortmund, Germany, (A.Z.); , (J.R.); (D.D.)
| | - Walaa Murad
- Histology Department, Faculty of Medicine, South Valley University, Qena 83523, Egypt; (W.M.); (T.A.); (E.A.A.)
| | - Reham Hassan
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, 44139 Dortmund, Germany, (A.Z.); , (J.R.); (D.D.)
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Yasser A. Ahmed
- Department of Histology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt;
| | - Tahany Abbas
- Histology Department, Faculty of Medicine, South Valley University, Qena 83523, Egypt; (W.M.); (T.A.); (E.A.A.)
| | - Eman A. Abdelrahim
- Histology Department, Faculty of Medicine, South Valley University, Qena 83523, Egypt; (W.M.); (T.A.); (E.A.A.)
| | - Kai Markus Schneider
- Department of Medicine III, University Hospital RWTH Aachen, Aachen University, 52074 Aachen, Germany; (K.M.S.); (M.-L.B.); (M.H.); (C.T.)
| | - Madlen Matz-Soja
- Faculty of Medicine, Rudolf-Schönheimer-Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany; (M.M.-S.); (R.G.)
| | - Jörg Reinders
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, 44139 Dortmund, Germany, (A.Z.); , (J.R.); (D.D.)
| | - Rolf Gebhardt
- Faculty of Medicine, Rudolf-Schönheimer-Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany; (M.M.-S.); (R.G.)
| | - Marie-Luise Berres
- Department of Medicine III, University Hospital RWTH Aachen, Aachen University, 52074 Aachen, Germany; (K.M.S.); (M.-L.B.); (M.H.); (C.T.)
| | - Maximilian Hatting
- Department of Medicine III, University Hospital RWTH Aachen, Aachen University, 52074 Aachen, Germany; (K.M.S.); (M.-L.B.); (M.H.); (C.T.)
| | - Dirk Drasdo
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, 44139 Dortmund, Germany, (A.Z.); , (J.R.); (D.D.)
- Modelling and Analysis for Medical and Biological Applications (MAMBA), Inria Paris & Sorbonne Université LJLL, 2 Rue Simone IFF, 75012 Paris, France
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Institute of Computational Biomedicine, Heidelberg University, Bioquant—Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; (C.H.H.); (J.S.-R.)
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Pauwelsstrasse 19, 52074 Aachen, Germany
| | - Christian Trautwein
- Department of Medicine III, University Hospital RWTH Aachen, Aachen University, 52074 Aachen, Germany; (K.M.S.); (M.-L.B.); (M.H.); (C.T.)
| | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, 44139 Dortmund, Germany, (A.Z.); , (J.R.); (D.D.)
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Tajti F, Kuppe C, Antoranz A, Ibrahim MM, Kim H, Ceccarelli F, Holland CH, Olauson H, Floege J, Alexopoulos LG, Kramann R, Saez-Rodriguez J. A Functional Landscape of CKD Entities From Public Transcriptomic Data. Kidney Int Rep 2019; 5:211-224. [PMID: 32043035 PMCID: PMC7000845 DOI: 10.1016/j.ekir.2019.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/09/2019] [Accepted: 11/04/2019] [Indexed: 12/18/2022] Open
Abstract
Introduction To develop effective therapies and identify novel early biomarkers for chronic kidney disease, an understanding of the molecular mechanisms orchestrating it is essential. We here set out to understand how differences in chronic kidney disease (CKD) origin are reflected in gene expression. To this end, we integrated publicly available human glomerular microarray gene expression data for 9 kidney disease entities that account for most of CKD worldwide. Our primary goal was to demonstrate the possibilities and potential on data analysis and integration to the nephrology community. Methods We integrated data from 5 publicly available studies and compared glomerular gene expression profiles of disease with that of controls from nontumor parts of kidney cancer nephrectomy tissues. A major challenge was the integration of the data from different sources, platforms, and conditions that we mitigated with a bespoke stringent procedure. Results We performed a global transcriptome-based delineation of different kidney disease entities, obtaining a transcriptomic diffusion map of their similarities and differences based on the genes that acquire a consistent differential expression between each kidney disease entity and nephrectomy tissue. We derived functional insights by inferring the activity of signaling pathways and transcription factors from the collected gene expression data and identified potential drug candidates based on expression signature matching. We validated representative findings by immunostaining in human kidney biopsies indicating, for example, that the transcription factor FOXM1 is significantly and specifically expressed in parietal epithelial cells in rapidly progressive glomerulonephritis (RPGN) whereas not expressed in control kidney tissue. Furthermore, we found drug candidates by matching the signature on expression of drugs to that of the CKD entities, in particular, the Food and Drug Administration-approved drug nilotinib. Conclusion These results provide a foundation to comprehend the specific molecular mechanisms underlying different kidney disease entities that can pave the way to identify biomarkers and potential therapeutic targets. To facilitate further use, we provide our results as a free interactive Web application: https://saezlab.shinyapps.io/ckd_landscape/. However, because of the limitations of the data and the difficulties in its integration, any specific result should be considered with caution. Indeed, we consider this study rather an illustration of the value of functional genomics and integration of existing data.
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Affiliation(s)
- Ferenc Tajti
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Christoph Kuppe
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Asier Antoranz
- Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece.,Department of Testing Services, ProtATonce Ltd., Athens, Greece
| | - Mahmoud M Ibrahim
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Hyojin Kim
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany
| | - Francesco Ceccarelli
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany
| | - Christian H Holland
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Institute for Computational Biomedicine, Heidelberg University, Bioquant, Heidelberg, Germany
| | - Hannes Olauson
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Jürgen Floege
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Leonidas G Alexopoulos
- Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece.,Department of Testing Services, ProtATonce Ltd., Athens, Greece
| | - Rafael Kramann
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine, RWTH Aachen University, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Aachen, Germany.,Institute for Computational Biomedicine, Heidelberg University, Bioquant, Heidelberg, Germany
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Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J. Benchmark and integration of resources for the estimation of human transcription factor activities. Genome Res 2019; 29:1363-1375. [PMID: 31340985 PMCID: PMC6673718 DOI: 10.1101/gr.240663.118] [Citation(s) in RCA: 381] [Impact Index Per Article: 76.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 05/28/2019] [Indexed: 12/25/2022]
Abstract
The prediction of transcription factor (TF) activities from the gene expression of their targets (i.e., TF regulon) is becoming a widely used approach to characterize the functional status of transcriptional regulatory circuits. Several strategies and data sets have been proposed to link the target genes likely regulated by a TF, each one providing a different level of evidence. The most established ones are (1) manually curated repositories, (2) interactions derived from ChIP-seq binding data, (3) in silico prediction of TF binding on gene promoters, and (4) reverse-engineered regulons from large gene expression data sets. However, it is not known how these different sources of regulons affect the TF activity estimations and, thereby, downstream analysis and interpretation. Here we compared the accuracy and biases of these strategies to define human TF regulons by means of their ability to predict changes in TF activities in three reference benchmark data sets. We assembled a collection of TF-target interactions for 1541 human TFs and evaluated how different molecular and regulatory properties of the TFs, such as the DNA-binding domain, specificities, or mode of interaction with the chromatin, affect the predictions of TF activity. We assessed their coverage and found little overlap on the regulons derived from each strategy and better performance by literature-curated information followed by ChIP-seq data. We provide an integrated resource of all TF-target interactions derived through these strategies, with confidence scores, as a resource for enhanced prediction of TF activities.
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Affiliation(s)
- Luz Garcia-Alonso
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, CB10 1SD Cambridge, United Kingdom
- Open Targets, Wellcome Genome Campus, CB10 1SD Cambridge, United Kingdom
| | - Christian H Holland
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany
- Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine, 69120 Heidelberg, Germany
| | - Mahmoud M Ibrahim
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany
- Department of Nephrology, RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany
| | - Denes Turei
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany
- Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine, 69120 Heidelberg, Germany
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, CB10 1SD Cambridge, United Kingdom
- Open Targets, Wellcome Genome Campus, CB10 1SD Cambridge, United Kingdom
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany
- Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine, 69120 Heidelberg, Germany
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Affiliation(s)
- C K Goldman
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47906, USA.
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Bouloy RP, Lappin MR, Holland CH, Thrall MA, Baker D, O'Neil S. Clinical ehrlichiosis in a cat. J Am Vet Med Assoc 1994; 204:1475-8. [PMID: 8050974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Clinical ehrlichiosis was diagnosed in a cat from Colorado on the basis of cytologic, serologic, and clinical findings. Clusters of gram-negative organisms that were morphologically similar to morulae of Ehrlichia spp were found only in mononuclear cells. The cat had clinical signs that were referable to infection by a rickettsial organism, and antibodies against E canis (titer, 1:80) and E risticii (titer, 1:40) were detected in serum. Exclusion of other obvious causes inducing similar clinical signs, and positive clinical response to doxycycline, an antibiotic with known antirickettsial actions, aided in diagnosis. The cat was clinically normal within days following initiation of treatment, and was clinically normal, as well as seronegative for antibodies against E canis and E risticii, 1,365 days after discharge.
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Affiliation(s)
- R P Bouloy
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins 80523
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Feinberg H, Levitsky S, Coughlin TR, Merchant F, Holland CH, O'Donaghue M. Effect of dipyridamole on ischemia-induced changes in cardiac performance and metabolism. J Cardiovasc Pharmacol 1980; 2:299-307. [PMID: 6156327 DOI: 10.1097/00005344-198005000-00007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The effect of the coronary vasocilator agents dipyridamole and nifedapine on ischemia-induced changes in cardiac performance and coronary flow was studied in extra-corporeal-circulation supported, open-chest dogs during cardio-pulmonary bypass. Coronary flow and isovolumic cardiac performance were measured prior to clamping the aorta to induce global ischemic for 60 min and again after 30 min of reperfusion. Both agents given prior to ischemia significantly enhanced the coronary flow measured 30 min after reperfusion. Almost complete complete return of pre-ischemic left ventricular dp/dt and diastolic compliance was seen if dipyridamole was administered prior to the onset of ischemia. Dipridamole administered at the end of the ischemic period and prior to reperfusion also prevented the ischemia-induced fall in dp/dt but not the decrease in compliance. Myocardial high energy phosphate compounds decreased markedly during global ischemia and dipyridamole administration had no effect on the rate or extent of their depletion. Nifedapine administration led to even greater post-ischemic coronary vasodilation; however, the ischemia-induced decline in myocardial performance was not prevented.
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Reznikoff M, Holland CH, Stroebel CF. Attitudes toward computers among employees of a psychiatric hospital. Ment Hyg 1967; 51:419-25. [PMID: 6057531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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